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拷贝数签名分析工具及其在前列腺癌中的应用揭示了不同的突变过程和临床结局。

Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.

机构信息

School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.

出版信息

PLoS Genet. 2021 May 4;17(5):e1009557. doi: 10.1371/journal.pgen.1009557. eCollection 2021 May.

DOI:10.1371/journal.pgen.1009557
PMID:33945534
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8121287/
Abstract

Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers for the progression of multiple cancer. However, practical tools for studying the signatures of copy number alterations are still lacking. Here, a user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization. This tool has been applied in prostate cancer (PC), which is particularly driven by complex genome alterations. Five copy number signatures are identified from human PC genome with this tool. The underlying mutational processes for each copy number signature have been illustrated. Sample clustering based on copy number signature exposure reveals considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. This copy number signature analysis in PC provides distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis.

摘要

基因组改变特征反映了癌症演化过程中由不同内源性或外源性突变事件引起的反复出现的模式。单碱基替换 (SBS) 的特征已在不同类型的癌症中得到广泛研究。拷贝数改变是多种癌症进展的重要驱动因素。然而，用于研究拷贝数改变特征的实用工具仍然缺乏。在这里，构建了一个用户友好的开源生物信息学工具“sigminer”，用于拷贝数特征的提取、分析和可视化。该工具已应用于前列腺癌 (PC)，其特别受到复杂基因组改变的驱动。使用此工具从人类 PC 基因组中鉴定出五个拷贝数特征。已经说明了每个拷贝数特征的潜在突变过程。基于拷贝数特征暴露的样本聚类揭示了 PC 的相当大的异质性，并且与 SBS 特征相比，拷贝数特征显示出改善的 PC 临床结果相关性。PC 中的这种拷贝数特征分析为 PC 的病因学提供了独特的见解，并为 PC 分层和预后提供了潜在的生物标志物。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/699e125fd2c0/pgen.1009557.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/f6d7339e3677/pgen.1009557.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/e36b7c2aca80/pgen.1009557.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/abda0fcd6c15/pgen.1009557.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/75f0a3826ce8/pgen.1009557.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/f889a508a877/pgen.1009557.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/699e125fd2c0/pgen.1009557.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/f6d7339e3677/pgen.1009557.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/e36b7c2aca80/pgen.1009557.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/abda0fcd6c15/pgen.1009557.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/75f0a3826ce8/pgen.1009557.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/f889a508a877/pgen.1009557.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f45/8121287/699e125fd2c0/pgen.1009557.g006.jpg

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